- This record was updated by the submitter. Please see the current version.
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) AND Immunodeficiency, common variable, 2
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000005623.37
Allele description
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)
- Gene:
- TNFRSF13B:TNF receptor superfamily member 13B [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 17p11.2
- Genomic location:
- Preferred name:
- NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)
- HGVS:
- NC_000017.11:g.16948873A>G
- NG_007281.1:g.28216T>C
- NM_012452.3:c.310T>CMANE SELECT
- NP_036584.1:p.Cys104Arg
- NP_036584.1:p.Cys104Arg
- LRG_120t1:c.310T>C
- LRG_120:g.28216T>C
- LRG_120p1:p.Cys104Arg
- NC_000017.10:g.16852187A>G
- NM_012452.2:c.310T>C
- NM_012452.3:c.310T>C
- O14836:p.Cys104Arg
- p.(Cys104Arg)
This HGVS expression did not pass validation- Protein change:
- C104R; CYS104ARG
- Links:
- UniProtKB: O14836#VAR_024027; OMIM: 604907.0001; dbSNP: rs34557412
- NCBI 1000 Genomes Browser:
- rs34557412
- Molecular consequence:
- NM_012452.3:c.310T>C - missense variant - [Sequence Ontology: SO:0001583]
- Observations:
- 8
Condition(s)
- Name:
- Immunodeficiency, common variable, 2
- Synonyms:
- ANTIBODY DEFICIENCY DUE TO TACI DEFECT; HYPOGAMMAGLOBULINEMIA DUE TO TACI DEFICIENCY; Hypogamma-globulinemia, acquired; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0009413; MedGen: C3150354; Orphanet: 1572; OMIM: 240500
-
ovule-2
ovule-2biosample
-
actin, partial [Cercospora aff. canescens]
actin, partial [Cercospora aff. canescens]gi|2314345808|gb|UXX22619.1|Protein
-
Absent epiphyses
Absent epiphysesMedGen
-
C4021862[conceptid] (1)
MedGen
-
Chain E, Peptide from Protein numb homolog
Chain E, Peptide from Protein numb homologgi|1345621988|pdb|5YQG|EProtein
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See more...Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000025805 | OMIM | no assertion criteria provided | Pathogenic (Jun 1, 2007) | germline | literature only | |
SCV000255489 | UCLA Clinical Genomics Center, UCLA - CES | criteria provided, single submitter (Lee et al. (JAMA. 2014)) | Likely pathogenic (Jul 15, 2014) | germline | clinical testing | |
SCV000590895 | Center of Genomic medicine, Geneva, University Hospital of Geneva | criteria provided, single submitter (ACMG Guidelines, 2015) | risk factor (Jun 7, 2017) | maternal | clinical testing | |
SCV000649856 | Invitae | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Likely pathogenic (Jan 31, 2024) | germline | clinical testing | |
SCV001427230 | Clinical Genomics Laboratory, Stanford Medicine | no assertion criteria provided | Uncertain significance (Mar 24, 2020) | germline | clinical testing | |
SCV001448757 | Knight Diagnostic Laboratories, Oregon Health and Sciences University | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Sep 6, 2019) | germline | clinical testing | |
SCV001530692 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | unknown | clinical testing | |
SCV001837633 | Suma Genomics | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance | unknown | clinical testing | |
SCV001934352 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Dec 3, 2020) | unknown | clinical testing | |
SCV001976896 | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Oct 6, 2021) | unknown | clinical testing | |
SCV002058245 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 3, 2022) | germline | clinical testing | PubMed (1) PMID:21419480, |
SCV002519879 | Mendelics | criteria provided, single submitter (Mendelics Assertion Criteria 2019) | Pathogenic (May 4, 2022) | germline | clinical testing | |
SCV002568305 | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Apr 26, 2022) | germline | clinical testing | |
SCV002759354 | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Dec 7, 2022) | germline | clinical testing | |
SCV002764634 | Department of Pathology and Laboratory Medicine, Sinai Health System | no assertion criteria provided | Established risk allele | unknown | research | |
SCV003807042 | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Dec 22, 2022) | germline | clinical testing | |
SCV004046269 | Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic | germline | clinical testing | |
SCV005077735 | Institute of Immunology and Genetics Kaiserslautern | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 2, 2024) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | yes | 7 | not provided | not provided | 7 | not provided | clinical testing |
not provided | germline | unknown | 1 | not provided | not provided | not provided | not provided | clinical testing |
not provided | maternal | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, research |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
Citations
PubMed
TACI is mutant in common variable immunodeficiency and IgA deficiency.
Castigli E, Wilson SA, Garibyan L, Rachid R, Bonilla F, Schneider L, Geha RS.
Nat Genet. 2005 Aug;37(8):829-34. Epub 2005 Jul 10.
- PMID:
- 16007086
Garibyan L, Lobito AA, Siegel RM, Call ME, Wucherpfennig KW, Geha RS.
J Clin Invest. 2007 Jun;117(6):1550-7. Epub 2007 May 10.
- PMID:
- 17492055
- PMCID:
- PMC1865037
Details of each submission
From OMIM, SCV000025805.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (3) |
Description
In a mother and son with common variable immunodeficiency-2 (240500), Castigli et al. (2005) identified a heterozygous 310T-C transition in exon 3 of the TNFRSF13B gene that resulted in a cys104-to-arg (C104R) substitution in the extracellular domain of TACI. Another unrelated woman with CVID2 was compound heterozygous for C104R and a single-basepair insertion (604907.0004). She inherited the C104R mutation from her father, who had selective immunoglobulin A deficiency-2 (609529), and transmitted the heterozygous C104R mutation to her son, who had CVID2. The proband's 2 sisters, who had IGAD2, were also heterozygous for the mutation. Heterozygosity for C104R was also found in 4 members of a third family with IGAD2. Studies of patient B cells showed that the mutant protein was expressed on the surface, but was unable to bind the ligand BAFF (603969); stimulation with APRIL (604472) failed to stimulate IgA or IgG secretion from B cells.
Salzer et al. (2005) identified the C104R mutation in affected members of a family with multiple cases of humoral immunodeficiency; 3 individuals who were heterozygous for the mutation had IGAD2, whereas 1 individuals who was homozygous for the mutation had CVID2. In addition, 2 unrelated patients with sporadic CVID were heterozygous for the mutation. Transformed B lymphocytes from patients showed severely compromised binding to APRIL and compromised B-cell proliferation; APRIL and BAFF failed to induce class-switch recombination in TACI-deficient B cells. Salzer et al. (2005) referred to the nucleotide substitution as 323T-C. The authors suggested that the incomplete penetrance of TACI mutations may reflect partial redundancy of the system.
Using in vitro transfection assays, Garibyan et al. (2007) showed that the C104R mutation, as well as its murine counterpart (C76R), interfered with TACI signaling in a dominant manner that was dependent on preassociation of C104R mutant TACI with wildtype TACI in the absence of ligand. Ligand was able to bind wildtype TACI, suggesting that C104R disrupts ligand-induced receptor rearrangement and signaling. These findings revealed that TACI preassembles as a homotypic oligomeric complex before binding ligand and provided a mechanism for how the heterozygous C104R mutation leads to CVID.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From UCLA Clinical Genomics Center, UCLA - CES, SCV000255489.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000590895.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | maternal | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Invitae, SCV000649856.7
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (11) |
Description
This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 104 of the TNFRSF13B protein (p.Cys104Arg). This variant is present in population databases (rs34557412, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with common variable immunodeficiency (CVID) (PMID: 16007087, 17392797, 19779048, 22697072, 24051380, 27123465). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5302). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TNFRSF13B protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TNFRSF13B function (PMID: 16007087, 20889194, 21419480, 21458042, 23237420, 24051380). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Clinical Genomics Laboratory, Stanford Medicine, SCV001427230.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | clinical testing | not provided |
Description
The p.Cys104Arg variant in the TNFRSF13B gene has been previously reported in the heterozygous, compound heterozygous, or homozygous state in many individuals with common variable immunodeficiency (CVID; Castigli et al., 2005; de Valles-Ibáñez et al., 2018; Martinez-Polmar et al., 2009; Salzer et al., 2005). The p.Cys104Arg variant has also been identified in 697/129,190 European chromosomes, including 3 homozygotes, by the Genome Aggregation Database (http://gnomad.broadinstitute.org/), indicating it may be a common, reduced penetrance allele. The p.Cys104Arg variant is relatively common in the general population, and case-control studies provide conflicting evidence for an association with antibody deficiency (Castigli 2005; de VallesIbanez 2018; Pan-Hammarström et al, 2007; Pulvirenti et al., 2016; Salzer et al., 2009). Functional studies have shown that this variant impairs ligand binding, B cell proliferation, and antibody responses (Castigli et al., 2005; Fried et al., 2011; Lee et al., 2010; Salzer et al., 2005). Computational tools predict that the p.Cys104Arg variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Cys104Arg variant is uncertain; however, there is suspicion that this variant could be associated with common variable immunodeficiency due to functional studies and the predicted impact to the protein. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PS3_moderate; PP3]
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448757.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Baylor Genetics, SCV001530692.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Suma Genomics, SCV001837633.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001934352.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976896.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PM2, PM5, PP3, PP5
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From 3billion, SCV002058245.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000005302, PS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 21419480, 20889194, PS3_S). A different missense change at the same codon (p.Cys104Tyr) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000645207, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.919, 3CNET: 0.974, PP3_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Mendelics, SCV002519879.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002568305.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PS3 PM1 PP3
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV002759354.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Department of Pathology and Laboratory Medicine, Sinai Health System, SCV002764634.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | not provided |
Description
The TNFRSF13B c.310T>C (p.Cys104Arg) variant has been reported in >50 homozygous, heterozygous, and compound heterozygous individuals with common variable immune deficiency (CVID), as well as in multiple healthy individuals (Salzer_2009_PMID: 18981294; Barroeta Seijas_2012_PMID: 22697072; Martinez-Gallo_2013_PMID: 23237420; Lee_2010_PMID: 20889194; Pulvirenti_2016_PMID: 27123465; Freiberger_2012_PMID: 22884984). In addition, this variant segregated with disease in at least 13 members from 7 families; however, asymptomatic homozygous and heterozygous family members were also identified, suggesting incomplete penetrance (Salzer_2009_PMID: 18981294; Barroeta Seijas_2012_PMID: 22697072; Martinez-Gallo_2013_PMID: 23237420; Koopmans_2013_PMID: 22983507). The variant was identified in dbSNP (ID: rs34557412) and ClinVar (classified as pathogenic by GeneDx and two other submitters, as likely pathogenic by Invitae and three other submitters, as uncertain significance by Laboratory for Molecular Medicine and five other submitters, as likely benign by Illumina and one other submitter, and as 'risk factor' by University Hospital of Geneva). The variant was identified in control databases in 983 of 282890 chromosomes (4 homozygous) at a frequency of 0.00347, and was observed at the highest frequency in the European (non-Finnish) population in 697 of 129190 chromosomes (freq: 0.005395) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.C104 residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) suggest that the variant may impact the protein. Furthermore, multiple in vitro functional studies and murine models reveal that this variants leads to decreased protein surface expression, decreased antibody response, and impaired ligand binding ability compared to wildtype (Salzer_2009_PMID: 18981294; Martinez-Gallo_2013_PMID: 23237420; Lee_2010_PMID: 20889194; Bacchelli_2011_PMID: 21458042). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI) do not predict a deleterious effect on splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic - risk factor for common variable immunodeficiency.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003807042.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
2 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
3 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
4 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
5 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
6 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
ACMG classification criteria: PS3 supporting, PM3 moderated, PP1 moderated, PP3 supporting
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
2 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
3 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
4 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
5 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
6 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046269.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This is a recurrent variant that has been reported as homozygous, compound heterozygous, and heterozygous change in individuals with common variable immunodeficiency (CVID) and in unaffected control individuals (PMID: 23237420, 17392797, 20156508, 24051380, 16007086, 16007087, 22884984). A study of 844 cases with CVID and 3924 controls found the p.Cys104Arg variant significantly enriched in cases versus controls (OR 5.60, CI 2.99-10.51, p=3.9 x 10-8) (PMID: 17392797). Further, a meta-analysis of 1,439 CVID patients and 3,558 controls confirmed enrichment of this variant in CVID cases versus controls (p < 10-5) (PMID: 22884984). In-vitro studies showed that the variant, which is located in the transmembrane (TM) domain of TACI, disrupts NF-kB/NF-AT signaling and leads to defective B-cell proliferation in response to stimulation (PMID: 21419480, 23237420, 19605846). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.35% (983/282890) and in the homozygote state in 4 individuals. The c.310T>C (p.Cys104Arg) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.310T>C (p.Cys104Arg) variant is classified as Likely Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Immunology and Genetics Kaiserslautern, SCV005077735.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
ACMG Criteria: PS3, PS4, PM1, PM3, PM5, PP1, PP3, PP5; Variant was found in heterozygous state
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Sep 16, 2024